Two West Virginia coal-mining units owned by Alpha Natural Resources Inc. polluted streams and damaged aquatic ecosystems, a judge said, ruling in favor of three environmental groups that filed a citizen complaint.

U.S. District Judge Robert Chambers’s June 4 decision sets the stage for possible injunctions and civil penalties. The judge found that the mine operators, Alex Energy Inc. and Elk Run Coal Co., discharged high levels of pollution into Laurel Creek and Robinson Fork.

“In multiple ways, the chemical and the biological components of the aquatic ecosystems found in Laurel Creek and Robinson Fork have been significantly adversely affected by the defendants’ discharges,” Chambers in Huntington, West Virginia, said in his ruling.

Elk Run owns and operates the White Castle No. 1 surface mine and the East of Stollings surface mine, both in the state’s Boone County. Alex Energy operates the Robinson North surface mine and the Wildcat surface mine, both in Nicholas County, according to the ruling.

Alpha Natural will appeal the ruling and expects “to see it reversed,” Ted Pile, a spokesman for the Bristol, Virginia-based company, said in an e-mail.

“This decision essentially strips the state of West Virginia of its legitimate role as the primary regulatory authority for state waters and substitutes in its place the federal court as the primary authority,” Pile said. “That’s clearly not the intent of the Clean Water Act.”

Alpha Natural is the second-largest U.S. coal producer, behind only Peabody Energy Corp.

The case is Ohio Valley Environmental Coalition v. Elk Run Coal Co., 12-cv-00785, U.S. District Court, Southern District of West Virginia (Huntington).